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Danzey LM, Briceño VF, Cook AM, Nicotra AB, Peyre G, Rossetto M, Yap JYS, Leigh A. Environmental and Biogeographic Drivers behind Alpine Plant Thermal Tolerance and Genetic Variation. PLANTS (BASEL, SWITZERLAND) 2024; 13:1271. [PMID: 38732486 PMCID: PMC11085172 DOI: 10.3390/plants13091271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
In alpine ecosystems, elevation broadly functions as a steep thermal gradient, with plant communities exposed to regular fluctuations in hot and cold temperatures. These conditions lead to selective filtering, potentially contributing to species-level variation in thermal tolerance and population-level genetic divergence. Few studies have explored the breadth of alpine plant thermal tolerances across a thermal gradient or the underlying genetic variation thereof. We measured photosystem heat (Tcrit-hot) and cold (Tcrit-cold) thresholds of ten Australian alpine species across elevation gradients and characterised their neutral genetic variation. To reveal the biogeographical drivers of present-day genetic signatures, we also reconstructed temporal changes in habitat suitability across potential distributional ranges. We found intraspecific variation in thermal thresholds, but this was not associated with elevation, nor underpinned by genetic differentiation on a local scale. Instead, regional population differentiation and considerable homozygosity within populations may, in part, be driven by distributional contractions, long-term persistence, and migrations following habitat suitability. Our habitat suitability models suggest that cool-climate-distributed alpine plants may be threatened by a warming climate. Yet, the observed wide thermal tolerances did not reflect this vulnerability. Conservation efforts should seek to understand variations in species-level thermal tolerance across alpine microclimates.
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Affiliation(s)
- Lisa M. Danzey
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway, NSW 2007, Australia;
| | - Verónica F. Briceño
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia; (V.F.B.); (A.B.N.)
| | - Alicia M. Cook
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway, NSW 2007, Australia;
| | - Adrienne B. Nicotra
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia; (V.F.B.); (A.B.N.)
| | - Gwendolyn Peyre
- Department of Civil and Environmental Engineering, University of the Andes, Bogota 111711, Colombia;
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Sydney, NSW 2000, Australia; (M.R.); (J.-Y.S.Y.)
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
| | - Jia-Yee S. Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Gardens Sydney, Sydney, NSW 2000, Australia; (M.R.); (J.-Y.S.Y.)
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrea Leigh
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia; (V.F.B.); (A.B.N.)
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2
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Schmidt DA, Galbreath KE, Russello MA. Phylogenomics of American pika (Ochotona princeps) lineage diversification. Mol Phylogenet Evol 2024; 193:108030. [PMID: 38341008 DOI: 10.1016/j.ympev.2024.108030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Quaternary climate oscillations have profoundly influenced current species distributions. For many montane species, these fluctuations were a prominent driver in species range shifts, often resulting in intraspecific diversification, as has been the case for American pikas (Ochotona princeps). Range shifts and population declines in this thermally-sensitive lagomorph have been linked to historical and contemporary environmental changes across its western North American range, with previous research reconstructing five mitochondrial DNA lineages. Here, we paired genome-wide data (25,244 SNPs) with range-wide sampling to re-examine the number and distribution of intra-specific lineages, and investigate patterns of within- and among-lineage divergence and diversity. Our results provide genomic evidence of O. princeps monophyly, reconstructing six distinct lineages that underwent multiple rounds of divergence (0.809-2.81 mya), including a new Central Rocky Mountain lineage. We further found evidence for population differentiation across multiple spatial scales, and reconstructed levels of standing variation comparable to those found in other small mammals. Overall, our findings demonstrate the influence of past glacial cycles on O. princeps lineage diversification, suggest that current subspecific taxonomy may need to be revisited, and provide an important framework for investigations of American pika adaptive potential in the face of anthropogenic climate change.
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Affiliation(s)
- Danielle A Schmidt
- Department of Biology, The University of British Columbia, Kelowna, BC, Canada
| | - Kurt E Galbreath
- Department of Biology, Northern Michigan University, Marquette, MI, USA
| | - Michael A Russello
- Department of Biology, The University of British Columbia, Kelowna, BC, Canada.
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Phylogeography of an endemic California silkmoth genus suggests the importance of an unheralded central California province in generating regional endemic biodiversity. Mol Phylogenet Evol 2021; 164:107256. [PMID: 34256128 DOI: 10.1016/j.ympev.2021.107256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/21/2022]
Abstract
The California Floristic province is a biodiversity hotspot. Understanding the phylogeographic patterns that exist in this diverse region is essential to understanding its evolution and for guiding conservation efforts. Calosaturnia is a charismatic silkmoth genus endemic to large portions of the region with three described species, C. mendocino, C. walterorum, and C. albofasciata. We sampled all three species from across their ranges, sequenced 1463 bp of mitochondrial COI and 1941 bp of nuclear DNA from three genes, and reconstructed phylogenetic relationships and estimated divergence times within the lineages. All three species show pronounced evidence of isolation and, in two cases, secondary reconnection. An unexpected monophyletic mtDNA lineage was found in the Central Coast region, in a region thought to represent an intergrade between C. mendocino and C. walterorum. Our genetic data also significantly revise previous hypotheses as to which species occur in which regions, suggesting that historical ecological changes around four Ma ago isolated some lineages, and a secondary isolation event two Ma ago led to isolation of populations both in the Central Coast region and the southern Sierra Nevada. Our results add to a currently under-appreciated pattern suggesting that coastal Central California is not a transition zone between Northern and Southern California Floristic Province faunas but rather its own unique, periodically isolated, biogeographic region. They also suggest cryptic diversity may be present in many other currently unrecognized groups. Additional research should focus on this central California region because many species may be highly restricted in range and in need of conservation attention.
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Weng YM, Kavanaugh DH, Schoville SD. Drainage basins serve as multiple glacial refugia for alpine habitats in the Sierra Nevada Mountains, California. Mol Ecol 2020; 30:826-843. [PMID: 33270315 DOI: 10.1111/mec.15762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/19/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022]
Abstract
The evolutionary histories of alpine species are often directly associated with responses to glaciation. Deep divergence among populations and complex patterns of genetic variation have been inferred as consequences of persistence within glacier boundaries (i.e., on nunataks), while shallow divergence and limited genetic variation are assumed to result from expansion from large refugia at the edge of ice shields (i.e., massifs de refuge). However, for some species, dependence on specific microhabitats could profoundly influence their spatial and demographic response to glaciation, and such a simple dichotomy may obscure the localization of actual refugia. In this study, we use the Nebria ingens complex (Coleoptera: Carabidae), a water-affiliated ground beetle lineage, to test how drainage basins are linked to their observed population structure. By analysing mitochondrial COI gene sequences and genome-wide single nucleotide polymorphisms, we find that the major drainage systems of the Sierra Nevada Mountains in California best explain the population structure of the N. ingens complex. In addition, we find that an intermediate morphotype within the N. ingens complex is the product of historical hybridization of N. riversi and N. ingens in the San Joaquin basin during glaciation. This study highlights the importance of considering ecological preferences in how species respond to climate fluctuations and provides an explanation for discordances that are often observed in comparative phylogeographical studies.
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Affiliation(s)
- Yi-Ming Weng
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - David H Kavanaugh
- Department of Entomology, California Academy of Sciences, San Francisco, CA, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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5
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Weng YM, Veire BM, Dudko RY, Medeiros MJ, Kavanaugh DH, Schoville SD. Rapid speciation and ecological divergence into North American alpine habitats: the Nippononebria (Coleoptera: Carabidae) species complex. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Abstract
The climate-driven species pump hypothesis has been supported in a number of phylogeographic studies of alpine species. Climate-driven shifts in distribution, coupled with rapid demographic change, have led to strong genetic drift and lineage diversification. Although the species pump has been linked to rapid speciation in a number of studies, few studies have demonstrated that ecological divergence accompanies rapid speciation. Here we examine genetic, morphological and physiological variation in members of the ground beetle taxon Nippononebria, to test three competing hypotheses of evolutionary diversification: isolation and incomplete lineage sorting (no speciation), recent speciation without ecological divergence, or recent speciation with ecological divergence into alpine habitats. Genetic data are consistent with recent divergence, with major lineages forming in the last million years. A species tree analysis, in conjunction with morphological divergence in male reproductive traits, support the formation of three recognized Nippononebria taxa. Furthermore, both morphological and physiological traits demonstrate ecological divergence in alpine lineages, with convergent shifts in body shape and thermal tolerance breadth. This provides strong evidence that the climate-driven species pump can generate ecological novelty, though it is argued that spatial scale may be a key determinant of broader patterns of macroevolution in alpine communities.
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Affiliation(s)
- Yi-Ming Weng
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Benton M Veire
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Roman Yu Dudko
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Tomsk State University, Tomsk, Russia
| | - Matthew J Medeiros
- Urban School of San Francisco, San Francisco, CA, USA
- School of Life Sciences, University of Nevada Las Vegas, S. Maryland Parkway, Las Vegas, NV, USA
| | - David H Kavanaugh
- Department of Entomology, California Academy of Sciences, San Francisco, CA, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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6
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Abstract
The enigmatic insect order Grylloblattodea comprises two described species in Canada, which are limited to the Montane Cordillera and Pacific Maritime ecozones. One of the described species has three Canadian subspecies of uncertain taxonomic ranking, and there are two additional undescribed or unreported species known in close proximity to the Canadian border in western Alberta and British Columbia that likely also occur in Canada. Thus, as much as 50% of the total taxonomic diversity of Grylloblattodea in Canada is still undocumented. Targeted surveys and taxonomic work, as well as studies that describe the ecology and conservation status of Grylloblattodea are important goals for future research.
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Affiliation(s)
- Sean D. Schoville
- University of Wisconsin-Madison, Department of Entomology, 1630 Linden Drive, 637 Russell Labs, Madison, Wisconsin 53706, USAUniversity of Wisconsin-MadisonMadisonUnited States of America
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7
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Lavin BR, Wogan GOU, McGuire JA, Feldman CR. Phylogeography of the Northern Alligator Lizard (Squamata, Anguidae): Hidden diversity in a western endemic. ZOOL SCR 2018. [DOI: 10.1111/zsc.12294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Brian R. Lavin
- Department of Biology; Sonoma State University; Rohnert Park California
| | - Guinevere O. U. Wogan
- Department of Environmental Science, Policy and Management and Museum of Vertebrate Zoology; University of California; Berkeley California
| | - Jimmy A. McGuire
- Department of Integrative Biology and Museum of Vertebrate Zoology; University of California; Berkeley California
| | - Chris R. Feldman
- Department of Biology and Program in Ecology, Evolution and Conservation Biology; University of Nevada; Reno Nevada
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8
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Starrett J, Hayashi CY, Derkarabetian S, Hedin M. Cryptic elevational zonation in trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus janus complex) from the California southern Sierra Nevada. Mol Phylogenet Evol 2018; 118:403-413. [DOI: 10.1016/j.ympev.2017.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 07/24/2017] [Accepted: 09/04/2017] [Indexed: 10/18/2022]
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9
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Rovito SM, Schoville SD. Testing models of refugial isolation, colonization and population connectivity in two species of montane salamanders. Heredity (Edinb) 2017. [PMID: 28635966 DOI: 10.1038/hdy.2017.31] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Pleistocene glaciations have profoundly affected patterns of genetic diversity within many species. Temperate alpine organisms likely experienced dramatic range shifts, given that much of their habitat was glaciated during this time. While the effects of glaciations are relatively well understood, the spatial locations of refugia and processes that gave rise to current patterns of diversity are less well known. We use a microsatellite data set to test hypotheses of population connectivity and refugial isolation in the web-toed salamanders (Hydromantes) of the Sierra Nevada. We reject models of refugia with subsequent expansion into either the high southern Sierra or low-elevation Owens Valley, in favor of a simple isolation model with no migration between current populations. We find no evidence of migration at even moderate spatial scales using a variety of analyses in the southern Sierra, and limited migration in the northern Sierra. These results suggest that divergence in isolation following fragmentation is the dominant process structuring genetic variation in these salamander species. In the context of anthropogenic climate change and habitat degradation, these results imply that salamanders and other low-vagility alpine organisms are at risk of decline as they are unlikely to migrate across large distances.
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Affiliation(s)
- S M Rovito
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.,Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Gto, México
| | - S D Schoville
- Université Joseph Fourier, Grenoble, Centre National de la Recherche Scientifique TIMC-IMAG UMR 5525, Equipe Biologie Computationnelle et Mathématique, Grenoble, France.,Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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10
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Cui Y, Béthoux O, Klass KD, Ren D. The Jurassic Bajanzhargalanidae (Insecta: Grylloblattida?): New genera and species, and data on postabdominal morphology. ARTHROPOD STRUCTURE & DEVELOPMENT 2015; 44:688-716. [PMID: 25979677 DOI: 10.1016/j.asd.2015.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 04/23/2015] [Accepted: 04/25/2015] [Indexed: 06/04/2023]
Abstract
The presumed phylogenetic link between extant ice-crawlers (Grylloblattidae = 'crown-Grylloblattida') and fossil species of the taxon concept Grylloblattida sensu Storozhenko (2002) is essentially based on postabdominal morphology. However, the fossil data are limited, and the interpretation is open to debate. Here we investigate a sample of a poorly known fossil 'grylloblattidan' family, the Bajanzhargalanidae, collected from the Daohugou locality (Middle Jurassic, China). We describe Sinonele fangi gen. nov., sp. nov., Sinonele hei gen. nov., sp. nov., Sinonele phasmoides gen. nov., sp. nov., and Sinonele mini gen. nov., sp. nov. Thanks to the abundance and exceptional preservation of the material, we could document wing venation intra-specific variability, provide cues to identify male and female individuals, describe and tentatively interpret various body structures of both sexes, and discuss them with a broad pterygotan phylogenetic perspective. The Bajanzhargalanidae exhibit a puzzling combination of postabdominal characters leaving us inconclusive on their affinities, or lack thereof, with crown-Grylloblattida. Our contribution suggests that a substantial effort will be needed to further investigate postabdominal structures from comparatively ancient fossil insects preserved as rock imprints, because of their broad morphological disparity.
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Affiliation(s)
- Yingying Cui
- College of Life Science, Capital Normal University, 10048 Beijing, China; Freiberg University of Mining and Technology, Institute of Geology, Department of Palaeontology, Bernhard-von-Cotta Str. 2, D-09599 Freiberg, Germany
| | - Olivier Béthoux
- Centre de Recherches sur la Paléobiodiversité et les Paléoenvironnements (CR2P, UMR 7207), Sorbonne Universités - MNHN, CNRS, UPMC-Paris6 - Muséum National d'Histoire Naturelle, 57 rue Cuvier, CP38, F-75005 Paris, France
| | - Klaus-Dieter Klass
- Senckenberg Natural History Collections Dresden, Königsbrücker Landstrasse 159, D-01109 Dresden, Germany
| | - Dong Ren
- College of Life Science, Capital Normal University, 10048 Beijing, China.
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Schoville SD, Slatyer RA, Bergdahl JC, Valdez GA. Conserved and narrow temperature limits in alpine insects: Thermal tolerance and supercooling points of the ice-crawlers, Grylloblatta (Insecta: Grylloblattodea: Grylloblattidae). JOURNAL OF INSECT PHYSIOLOGY 2015; 78:55-61. [PMID: 25956197 DOI: 10.1016/j.jinsphys.2015.04.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 04/17/2015] [Accepted: 04/20/2015] [Indexed: 06/04/2023]
Abstract
For many terrestrial species, habitat associations and range size are dependent on physiological limits, which in turn may influence large-scale patterns of species diversity. The temperature range experienced by individuals is considered to shape the breadth of the thermal niche, with species occupying temporally and/or geographically stable climates tolerating a narrow temperature range. High-elevation environments experience large temperature fluctuations, with frequent periods below 0 °C, but Grylloblatta (Grylloblattodea: Grylloblattidae) occupy climatically stable microhabitats within this region. Here we test critical thermal limits and supercooling points for five Grylloblatta populations from across a large geographic area, to examine whether the stable microhabitats of this group are associated with a narrow thermal niche and assess their capacity to tolerate cold conditions. Thermal limits are highly conserved in Grylloblatta, despite substantial genetic divergence among populations spanning 1500 m elevation and being separated by over 500 km. Further, Grylloblatta show exceptionally narrow thermal limits compared to other insect taxa with little capacity to improve cold tolerance via plasticity. In contrast, upper thermal limits were significantly depressed by cold acclimation. Grylloblatta maintain coordinated movement until they freeze, and they die upon freezing. Convergence of the critical thermal minima, supercooling point and lower lethal limits point to adaptation to a cold but, importantly, constant thermal environment. These physiological data provide an explanation for the high endemism and patchy distribution of Grylloblatta, which relies on subterranean retreats to accommodate narrow thermal limits. These retreats are currently buffered from temperature fluctuations by snow cover, and a declining snowpack thus places Grylloblatta at risk of exposure to temperatures beyond its tolerance capacity.
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Affiliation(s)
- Sean D Schoville
- University of Wisconsin-Madison, Department of Entomology, 1630 Linden Drive, Madison, WI 53706, USA.
| | - Rachel A Slatyer
- Department of Zoology, University of Melbourne, Parkville 3010, Australia
| | - James C Bergdahl
- Conservation Biology Center, University of the Wilderness, 919 S. Adams St., Spokane, WA 99204, USA
| | - Glenda A Valdez
- University of Wisconsin-Madison, Department of Entomology, 1630 Linden Drive, Madison, WI 53706, USA
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12
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Hedin M, Carlson D, Coyle F. Sky island diversification meets the multispecies coalescent - divergence in the spruce-fir moss spider (Microhexura montivaga, Araneae, Mygalomorphae) on the highest peaks of southern Appalachia. Mol Ecol 2015; 24:3467-84. [PMID: 26011071 DOI: 10.1111/mec.13248] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 05/13/2015] [Accepted: 05/14/2015] [Indexed: 01/31/2023]
Abstract
Microhexura montivaga is a miniature tarantula-like spider endemic to the highest peaks of the southern Appalachian mountains and is known only from six allopatric, highly disjunct montane populations. Because of severe declines in spruce-fir forest in the late 20th century, M. montivaga was formally listed as a US federally endangered species in 1995. Using DNA sequence data from one mitochondrial and seven nuclear genes, patterns of multigenic genetic divergence were assessed for six montane populations. Independent mitochondrial and nuclear discovery analyses reveal obvious genetic fragmentation both within and among montane populations, with five to seven primary genetic lineages recovered. Multispecies coalescent validation analyses [guide tree and unguided Bayesian Phylogenetics and Phylogeography (BPP), Bayes factor delimitation (BFD)] using nuclear-only data congruently recover six or seven distinct lineages; BFD analyses using combined nuclear plus mitochondrial data favour seven or eight lineages. In stark contrast to this clear genetic fragmentation, a survey of secondary sexual features for available males indicates morphological conservatism across montane populations. While it is certainly possible that morphologically cryptic speciation has occurred in this taxon, this system may alternatively represent a case where extreme population genetic structuring (but not speciation) leads to an oversplitting of lineage diversity by multispecies coalescent methods. Our results have clear conservation implications for this federally endangered taxon and illustrate a methodological issue expected to become more common as genomic-scale data sets are gathered for taxa found in naturally fragmented habitats.
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Affiliation(s)
- Marshal Hedin
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Dave Carlson
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
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13
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Slatyer RA, Nash MA, Miller AD, Endo Y, Umbers KDL, Hoffmann AA. Strong genetic structure corresponds to small-scale geographic breaks in the Australian alpine grasshopper Kosciuscola tristis. BMC Evol Biol 2014; 14:204. [PMID: 25273226 PMCID: PMC4203917 DOI: 10.1186/s12862-014-0204-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 09/17/2014] [Indexed: 12/21/2022] Open
Abstract
Background Mountain landscapes are topographically complex, creating discontinuous ‘islands’ of alpine and sub-alpine habitat with a dynamic history. Changing climatic conditions drive their expansion and contraction, leaving signatures on the genetic structure of their flora and fauna. Australia’s high country covers a small, highly fragmented area. Although the area is thought to have experienced periods of relative continuity during Pleistocene glacial periods, small-scale studies suggest deep lineage divergence across low-elevation gaps. Using both DNA sequence data and microsatellite markers, we tested the hypothesis that genetic partitioning reflects observable geographic structuring across Australia’s mainland high country, in the widespread alpine grasshopper Kosciuscola tristis (Sjösted). Results We found broadly congruent patterns of regional structure between the DNA sequence and microsatellite datasets, corresponding to strong divergence among isolated mountain regions. Small and isolated mountains in the south of the range were particularly distinct, with well-supported divergence corresponding to climate cycles during the late Pliocene and Pleistocene. We found mixed support, however, for divergence among other mountain regions. Interestingly, within areas of largely contiguous alpine and sub-alpine habitat around Mt Kosciuszko, microsatellite data suggested significant population structure, accompanied by a strong signature of isolation-by-distance. Conclusions Consistent patterns of strong lineage divergence among different molecular datasets indicate genetic breaks between populations inhabiting geographically distinct mountain regions. Three primary phylogeographic groups were evident in the highly fragmented Victorian high country, while within-region structure detected with microsatellites may reflect more recent population isolation. Despite the small area of Australia’s alpine and sub-alpine habitats, their low topographic relief and lack of extensive glaciation, divergence among populations was on the same scale as that detected in much more extensive Northern hemisphere mountain systems. The processes driving divergence in the Australian mountains might therefore differ from their Northern hemisphere counterparts. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0204-1) contains supplementary material, which is available to authorized users.
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14
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Australia's arid-adapted butcherbirds experienced range expansions during Pleistocene glacial maxima. Nat Commun 2014; 5:3994. [PMID: 24876071 DOI: 10.1038/ncomms4994] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/29/2014] [Indexed: 11/08/2022] Open
Abstract
A model of range expansions during glacial maxima (GM) for cold-adapted species is generally accepted for the Northern Hemisphere. Given that GM in Australia largely resulted in the expansion of arid zones, rather than glaciation, it could be expected that arid-adapted species might have had expanded ranges at GM, as cold-adapted species did in the Northern Hemisphere. For Australian biota, however, it remains paradigmatic that arid-adapted species contracted to refugia at GM. Here we use multilocus data and ecological niche models (ENMs) to test alternative GM models for butcherbirds. ENMs, mtDNA and estimates of nuclear introgression and past population sizes support a model of GM expansion in the arid-tolerant Grey Butcherbird that resulted in secondary contact with its close relative--the savanna-inhabiting Silver-backed Butcherbird--whose contemporary distribution is widely separated. Together, these data reject the universal use of a GM contraction model for Australia's dry woodland and arid biota.
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15
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Bidegaray-Batista L, Ferrández MÁ, Arnedo MA. Winter is coming: Miocene and Quaternary climatic shifts shaped the diversification of Western-MediterraneanHarpactocrates(Araneae, Dysderidae) spiders. Cladistics 2013; 30:428-446. [DOI: 10.1111/cla.12054] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2013] [Indexed: 01/26/2023] Open
Affiliation(s)
- Leticia Bidegaray-Batista
- Institut de Recerca de la Biodiversitat and Departament de Biologia Animal; Universitat de Barcelona; Av. Diagonal 643 Barcelona 08028 Spain
| | - Miguel Á. Ferrández
- Sociedad para el Estudio y la Conservación de las Arañas; c/Villafranca 24, 1_C Madrid 28028 Spain
| | - Miquel A. Arnedo
- Institut de Recerca de la Biodiversitat and Departament de Biologia Animal; Universitat de Barcelona; Av. Diagonal 643 Barcelona 08028 Spain
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16
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Parks DH, Mankowski T, Zangooei S, Porter MS, Armanini DG, Baird DJ, Langille MGI, Beiko RG. GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework. PLoS One 2013; 8:e69885. [PMID: 23922841 PMCID: PMC3726740 DOI: 10.1371/journal.pone.0069885] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/14/2013] [Indexed: 12/21/2022] Open
Abstract
GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis.
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Affiliation(s)
- Donovan H. Parks
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Timothy Mankowski
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Somayyeh Zangooei
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Michael S. Porter
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David G. Armanini
- Prothea srl, Milan, Italy
- Environment Canada @ Canadian Rivers Institute, University of New Brunswick, Fredericton, Canada
| | - Donald J. Baird
- Environment Canada @ Canadian Rivers Institute, University of New Brunswick, Fredericton, Canada
| | | | - Robert G. Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
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Cohen D. Conceptual models of the processes and patterns of the ecological, evolutionary and bio-geographical consequences of global climate changes. Isr J Ecol Evol 2013. [DOI: 10.1080/15659801.2013.929276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A unifying conceptual model is constructed for the major effects of alternating periods of global warming and cooling and sea-level changes on the geographical distributions and the ecological and genetic characteristics of species and ecological communities.
The main results found are:
The species in the interior of continuous global latitude and altitude temperature gradients are expected to follow the moving temperature zones without any major extinctions or any major changes in their physiological and ecological characteristics and adaptive roles during both global warming and global cooling periods, with competitive replacement of resident species by zonally dispersing pre-adapted species.
Many or all of the existing species at all the global cold boundary zones of both latitude and altitude temperature gradients are expected to become extinct during periods of global warming, which would be caused by competitive displacement by immigrating pre-adapted species from adjacent warmer zones.
Most existing species in the warm boundary zones of all the global temperature gradients are predicted to persist and adapt without competition to the increased temperature during periods of global warming, and to diversify by adaptations to newly created ecological opportunities.
Periods of global cooling are predicted to cause analogous opposite effects to the effects of global warming in the cold and warm boundaries of temperature gradients: that is, extinctions at the warm boundaries and persistence and adaptations at the cold boundaries:
Existing species in all islands and island-like isolated areas are predicted to persist in the absence of competitive displacement by immigrating pre-adapted species, and gradually adapt to the changing temperatures during periods of both global warming and global cooling.
During periods of global cooling, many more diverse opportunities for new adaptations and for invasions by pre-adapted species are expected and predicted in the large diversity of the newly open heterogeneous coldest and highest altitude zones of all the global altitude temperature gradients.
Long-term sequences of alternating periods of global warming and global cooling are expected to cancel and eliminate most of the ecological and adaptive changes which have occurred during the previous periods at all the latitude and altitude boundary zones. The species at the interior of continuous temperature gradients are expected to persist unchanged over long evolutionary time during repeated sequences of alternating periods of global warming and global cooling.
The effects of higher and lower global sea levels on the sea shore and intertidal species and communities during periods of global warming or cooling are expected to be analogous to the bio-geographical, ecological and genetic changes caused or predicted by global warming or cooling in the species and communities in terrestrial or marine temperature gradients.
Global sea-level changes which cause higher or lower shifting of the levels of the ecological zones in continuous sea shore gradients are expected therefore to cause continuous tracking and moving of the populations of the unchanged zonally adapted species. On the other hand, zonally adapted sea shore species are expected to be displaced or become extinct during periods of sea-level changes at the higher or lower boundary zones of the sea-level gradients in semi-isolated marine basins, and in locally discontinuous, fragmented or truncated sea shore ecological gradients.
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Affiliation(s)
- Dan Cohen
- Dept. of Ecology, Evolution, and Behaviour, The Silberman Institute of Life Sciences
- The Center for Rationality and Interactive Decisions, The Hebrew University of Jerusalem
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18
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Schoville SD, Uchifune T, Machida R. Colliding fragment islands transport independent lineages of endemic rock-crawlers (Grylloblattodea: Grylloblattidae) in the Japanese archipelago. Mol Phylogenet Evol 2012; 66:915-27. [PMID: 23220515 DOI: 10.1016/j.ympev.2012.11.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 11/09/2012] [Accepted: 11/23/2012] [Indexed: 11/24/2022]
Abstract
Fragment islands, viewed from the paradigm of island biogeographic theory, depend on continual immigration from continental sources to maintain levels of species diversity, or otherwise undergo a period of relaxation where species diversity declines to a lower equilibrium. Japan is a recently derived fragment island with a rich endemic flora and fauna. These endemic species have been described as paleoendemics, and conversely as recently derived Pleistocene colonists. Geological events in the Miocene period, notably the fragmentation and collision of islands, and the subsequent uplift of mountains in central Japan, provided opportunities for genetic isolation. More recently, cyclical climatic change during the Pliocene and Pleistocene periods led to intermittent land bridge connections to continental Asia. Here we investigate the pattern and timing of diversification in a diverse endemic lineage in order to test whether ongoing migration has sustained species diversity, whether there is evidence of relaxation, and how geological and climatic events are associated with lineage diversification. Using multi-locus genetic data, we test these hypotheses in a poorly dispersing, cold-adapted terrestrial insect lineage (Grylloblattodea: Grylloblattidae) sampled from Japan, Korea, and Russia. In phylogenetic analyses of concatenated data and a species tree approach, we find evidence of three deeply divergent lineages of rock-crawlers in Japan consistent with the pattern of island fragmentation from continental Asia. Tests of lineage diversification rates suggest that relaxation has not occurred and instead endemism has increased in the Japanese Grylloblattidae following mountain-building events in the Miocene. Although the importance of climate change in generating species diversity is a commonly held paradigm in Japanese biogeography, our analyses, including analyses of demographic change and phylogeographic range shifts in putative species, suggests that Pleistocene climatic change has had a limited effect on the diversification of rock-crawlers.
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Affiliation(s)
- Sean D Schoville
- Sugadaira Montane Research Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan.
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SCHOVILLE SEAND, LAM ATHENAW, RODERICK GEORGEK. A range-wide genetic bottleneck overwhelms contemporary landscape factors and local abundance in shaping genetic patterns of an alpine butterfly (Lepidoptera: Pieridae:Colias behrii). Mol Ecol 2012; 21:4242-56. [DOI: 10.1111/j.1365-294x.2012.05696.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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SCHOVILLE SEAND, RODERICK GEORGEK, KAVANAUGH DAVIDH. Testing the ‘Pleistocene species pump’ in alpine habitats: lineage diversification of flightless ground beetles (Coleoptera: Carabidae: Nebria) in relation to altitudinal zonation. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01911.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Kronauer DJC, Peters MK, Schöning C, Boomsma JJ. Hybridization in East African swarm-raiding army ants. Front Zool 2011; 8:20. [PMID: 21859477 PMCID: PMC3177866 DOI: 10.1186/1742-9994-8-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 08/22/2011] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Hybridization can have complex effects on evolutionary dynamics in ants because of the combination of haplodiploid sex-determination and eusociality. While hybrid non-reproductive workers have been found in a range of species, examples of gene-flow via hybrid queens and males are rare. We studied hybridization in East African army ants (Dorylus subgenus Anomma) using morphology, mitochondrial DNA sequences, and nuclear microsatellites. RESULTS While the mitochondrial phylogeny had a strong geographic signal, different species were not recovered as monophyletic. At our main study site at Kakamega Forest, a mitochondrial haplotype was shared between a "Dorylus molestus-like" and a "Dorylus wilverthi-like" form. This pattern is best explained by introgression following hybridization between D. molestus and D. wilverthi. Microsatellite data from workers showed that the two morphological forms correspond to two distinct genetic clusters, with a significant proportion of individuals being classified as hybrids. CONCLUSIONS We conclude that hybridization and gene-flow between the two army ant species D. molestus and D. wilverthi has occurred, and that mating between the two forms continues to regularly produce hybrid workers. Hybridization is particularly surprising in army ants because workers have control over which males are allowed to mate with a young virgin queen inside the colony.
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Affiliation(s)
- Daniel JC Kronauer
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- Laboratory of Insect Social Evolution, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Marcell K Peters
- Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Caspar Schöning
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- Länderinstitut für Bienenkunde, Friedrich-Engels-Strasse 32, 16540 Hohen Neuendorf, Germany
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
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22
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SCHOVILLE SEAND, STUCKEY MATTHEW, RODERICK GEORGEK. Pleistocene origin and population history of a neoendemic alpine butterfly. Mol Ecol 2011; 20:1233-47. [DOI: 10.1111/j.1365-294x.2011.05003.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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